Some possible reasons:
a) 3" are used more often now in the arcade (mostly golf and bowling games); maybe some are more used to that size.
b) 3" is bigger, and some follow the "bigger is better" saying.

c) 3" are heavier. This does make "whipping" it around a little harder, but lets it continue spinning longer after letting go. (One of my reasons; I have bad memories of gummed up trackballs that would stop the instant I let go.)
d) some of the not-as-old-as-classics games had two different control panel designs: 'standard' w/ 2 1/4", and a 'deluxe' w/ 3". I remember using the 'deluxe' at my local arcades of long ago.
e) 1up's "we were smaller when we played these games, so the trackball seemed bigger" was the third reason I got a 3" TB.
f) It's expense / space consuming / a hassle to have a 2 1/4" trackball cp for the old classics and a 3" tb cp for the newer classics. Instead of switching the cp depending on what game I was playing, I am going with only one size tb (for now

).
All personal reasons, for sure. [shrug]